You want Millenia's weapons to use hitman's animations? (That's how I understood it, I might be wrong)
If that's what you want to do, open the desired weapon's plugin in GECK. Now I assume vanilla weapons use hitman's animations - so just open a vanilla weapon by doubleclicking it, go to sound & animations tab and check which animations it uses (Reload type and weapon fire animation). Memorize them or write them down somewhere, exit the weapon's edit window, and open up the custom gun's edit window the same way. Switch to same animation set as the vanilla gun.
Might be obvious but still - note that you should find a corresponding weapon type when checking vanilla weapons' animation types. For example if you want Millenia's USP to use custom anims, check a 9mm or 10mm gun's animations and apply the same ones to the USP.